The problem with hitting a flush is they are relatively easy to sniff out in comparison to other big hands for decent players. Sometimes you don't get the big payoff you thought you were going to when you hit, and when you don't hit you could end up behind in eight ball in a tourney or SNG.
I agree. The implied odds aren't as great as say an open ended draw which is more well hidden and will probably get you paid off very nicely...
However,
Does your nut flush draw mean you're holding the Ace or is the Ace on the board and your holding the King?
Because if your holding the Ace, then that's 3 more outs added to your 9 which warrants a call of a standard bet. If your opponent paired, you're pretty much in a coin flip and could entertain the thought of reraising to put pressure back on your opponent. Even if your opponent flops 2 pair, you're only a 40% underdog not hit your flush or an Ace by the river. You're only really in trouble with flopped sets, trips or straights (boats and quads, you're dead meat anyway) which as you know are unlikely holdings. So a call or raise would be the move. I don't think I'd fold on the flop unless he put me all in.
If the Ace is already on the board, then I'll see what my opponent does and proceed accordingly. If he bets half the pot or less, I'm probably calling. As stated above, I don't think the implied odds warrant a call of a potsized bet because after seeing the third suit, I doubt I'd get paid off to justify the call.